Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T87325 Target Info
Target Name COVID-19 papain-like proteinase (PL-PRO)
Synonyms COVID-19 papain-like proteinase; COVID-19 PL2-PRO; COVID-19 PL-PRO; COVID-19 main proteinase; COVID-19 non-structural protein 3
Gene Name COVID-19 rep; COVID-19 1a-1b
Biochemical Class Coronaviruses polyprotein 1ab family
UniProt ID
R1AB_SARS2 (819 - 2763)
Ligand General Information  Top
Ligand Name Trifluoroacetic Acid Ligand Info
Canonical SMILES C(=O)(C(F)(F)F)O
InChI 1S/C2HF3O2/c3-2(4,5)1(6)7/h(H,6,7)
InChIKey DTQVDTLACAAQTR-UHFFFAOYSA-N
PubChem Compound ID 6422
Drug Binding Sites of Target  Top
PDB ID: 5RV1      PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000251609
Method X-ray diffraction Resolution 1.00 Å Mutation No [1]
PDB Sequence
VNSFSGYLKL
12
TDNVYIKNAD
22
IVEEAKKVKP
32
TVVVNAANVY
42
LKHGGGVAGA
52

LNKATNNAMQ
62
VESDDYIATN
72
GPLKVGGSCV
82
LSGHNLAKHC
92
LHVVGPNVNK
102

GEDIQLLKSA
112
YENFNQHEVL
122
LAPLLSAGIF
132
GADPIHSLRV
142
CVDTVRTNVY
152

LAVFDKNLYD
162
KLVSSFL
Residue
Distance (Å)
LEU126
3.173
ALA129
3.044
GLY130
2.986
PRO136
3.429
ALA154
4.076
Residue
Distance (Å)
VAL155
2.760
PHE156
1.942
ASP157
2.164
LEU160
2.722
LEU164
4.481
PDB ID: 5SRH      PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5265470867 - pyrimido-indole core only
Method X-ray diffraction Resolution 1.05 Å Mutation No [2]
PDB Sequence
VNSFSGYLKL
12
TDNVYIKNAD
22
IVEEAKKVKP
32
TVVVNAANVY
42
LKHGGGVAGA
52

LNKATNNAMQ
62
VESDDYIATN
72
GPLKVGGSCV
82
LSGHNLAKHC
92
LHVVGPNVNK
102

GEDIQLLKSA
112
YENFNQHEVL
122
LAPLLSAGIF
132
GADPIHSLRV
142
CVDTVRTNVY
152

LAVFDKNLYD
162
KLVSSFL
Residue
Distance (Å)
LEU126
2.876
ALA129
3.073
GLY130
3.028
PRO136
3.725
ALA154
4.030
Residue
Distance (Å)
VAL155
2.699
PHE156
2.029
ASP157
2.051
LEU160
2.730
LEU164
4.279
PDB ID: 5SRP      PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5340019182 - (R) isomer
Method X-ray diffraction Resolution 1.05 Å Mutation No [3]
PDB Sequence
VNSFSGYLKL
12
TDNVYIKNAD
22
IVEEAKKVKP
32
TVVVNAANVY
42
LKHGGGVAGA
52

LNKATNNAMQ
62
VESDDYIATN
72
GPLKVGGSCV
82
LSGHNLAKHC
92
LHVVGPNVNK
102

GEDIQLLKSA
112
YENFNQHEVL
122
LAPLLSAGIF
132
GADPIHSLRV
142
CVDTVRTNVY
152

LAVFDKNLYD
162
KLVSSFL
Residue
Distance (Å)
LEU126
3.234
ALA129
2.498
GLY130
2.985
PRO136
3.160
ALA154
4.236
Residue
Distance (Å)
VAL155
2.799
PHE156
2.542
ASP157
2.620
LEU160
2.457
LEU164
4.480
References  Top
REF 1 Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv. 2021 Apr 14;7(16):eabf8711.
REF 2 PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5265470867 - pyrimido-indole core only
REF 3 PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5340019182 - (R) isomer

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